|
| Status |
Public on Jan 01, 2012 |
| Title |
Per ZT12 rep2 non-polyA |
| Sample type |
SRA |
| |
|
| Source name |
Per ZT12 non-polyA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: per0
genetic background: Canton S
time point: ZT12
tissue: brain
amplification: Nugen (non polyA)
paired or single-end: paired (2x100)
mean insert size: 100 bp
|
| Treatment protocol |
brains were manually dissected in PBS at ZT0, ZT6, ZT12, and ZT18
|
| Growth protocol |
3-5 day old adult female flies were maintained on standard food and housed at 25 degrees in a 12hr:12hr light:dark environment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was purified using the PicoPure kit from MDS; RNA amplification and rRNA depletion was performed using the RiboAmp kit from MDS (polyA) and Ovation RNAseq kit from NuGEN (non polyA). Fragmentation, cDNA synthesis, and adaptor ligation was performed using standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011). The following parameters were used: "-limitBowtieNU -limitNU 25"
|
| |
|
| Submission date |
Jun 14, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Hughes |
| E-mail(s) |
michael.evan.hughes@gmail.com
|
| Organization name |
UPenn
|
| Street address |
421 Curie Bvd, Brb 835
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE29972 |
Deep sequencing the circadian transcriptome of Drosophila brain |
|
| Relations |
| Reanalyzed by |
GSM3274793 |
| SRA |
SRX082135 |
| BioSample |
SAMN00632305 |
